tbuckley/cabot-search huggingface dataset:
Abstract 189: Evaluating the influence of <i>Lactobacillus rhamnosus</i>-derived extracellular vesicles on calcium deposition in early breast cancer
Authors: Ngoc Bao Vuong, Melany Alomia, Intisar Alruwaili, Fahad Alsaab, James L. Erickson, Weidong Zhou, Alessandra Luchini, Monique Van Hoek, Virginia Espina, Richard A. Hoefer, Lance Liotta
Journal: Cancer Research (2022)

Abstract Microcalcifications are an important mammographic feature of ductal carcinoma in situ (DCIS) and are detected in 85-90% of abnormal mammograms. Calcium transport and calcium channels regulate microcalcifications and are essential for breast cancer proliferation. The breast duct intraductal lumen, which is the origin of ductal carcinomas, has been shown to be a non-sterile environment. We hypothesize that the intraductal microbiome influences calcium handling and mineral deposition in breast cancer. Bacteria have been known to enhance the formation of mineral deposits, including calcium salts, in various non mammalian microenvironments via secreted factors or extracellular vesicle mediated nucleation. We performed a clinical study on a cohort of 150 women who received a suspicious mammogram and were subjected to a follow up biopsy, and we identified differences in calcium handling microbiota between patients who harbored a malignant disease with respect to benign controls. To mechanistically study the role of microbiota in breast cancer calcium handling, we developed a 3D spheroid model of ductal carcinoma in situ using the BT-474 cell line. When exposed to high concentrations of calcium in the culture medium (from 1.75 mM to 2.05 mM), spheroids developed calcium mineral deposits in a calcium dose dependent manner; deposits were identified in internal regions of the spheroid, which correspond to hypoxic areas of DCIS in vivo. Extracellular calcium deposition correlated with cell survival in face of a toxic calcium level. Spheroids were cultured under a continuous flow of Lactobacillus rhamnosus LMS2-1-derived EVs over the course of two weeks. EVs were isolated by sequential ultracentrifugation; the 100K fraction was retained and characterized in terms of size, concentration, and protein content. EV treatment induced increased calcium export and mineral deposition in a dose dependent manner. Our findings support the hypothesis that L. rhamnosus-derived extracellular vesicles influence calcium regulation and mineral deposition in the hypoxic breast cancer milieu. More studies will be undertaken in the future to unveil molecular mechanisms that underlie this interaction, both at the cancer cell and the microbiota level. Citation Format: Ngoc Bao Vuong, Melany Alomia, Intisar Alruwaili, Fahad Alsaab, James L. Erickson, Weidong Zhou, Alessandra Luchini, Monique Van Hoek, Virginia Espina, Richard A. Hoefer, Lance Liotta. Evaluating the influence of Lactobacillus rhamnosus-derived extracellular vesicles on calcium deposition in early breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 189.
Abstract 3674: Differential expression of stress-survival pathway genes related to Hispanic colorectal cancer disparities
Authors: Aditi Kulkarni, Urbashi Basnet, Abhijeet R. Patil, Rebecca DeJesus, Sourav Roy
Journal: Cancer Research (2022)

Abstract Colorectal cancer (CRC) accounts for 12% and 8% of all estimated new cases of cancer and 11% and 9% of all cancer deaths in Hispanic men and women, respectively. Stress-survival pathways have been implicated in tumorigenesis of CRC and in providing resistance to chemotherapy-induced cell-death by suppressing reactive oxygen species (ROS), repairing DNA damage, and by regulating cell signaling pathways. However, studies related to the role of these pathways in CRC from the Hispanic health disparities perspective, are limited. Essential to improving treatment, prognosis, and detection strategies is the identification and validation of new ethnicity-specific transcriptomic markers within the stress-survival pathways as effective predictors of CRC. In this study, we have explored the role of stress-survival pathway genes in Hispanic and Non-Hispanic White (NHW) CRC tissues. We have used microarray and RNA-seq datasets obtained from the gene expression omnibus (GEO) and the cancer genome atlas (TCGA) to identify 28 genes associated with CRC. These genes were screened for transcript level expression in one normal colon and two CRC cell lines, and in cDNA arrays containing tumor (n=40) from different stages, and control (n=8) samples. The protein level expressions were evaluated by immunohistochemistry (IHC) in CRC tissue microarrays (TMAs) containing different stages of tumor (n = 108) and control (n = 12) tissues. All 28 genes were also analyzed for their transcript level expressions in Hispanic and NHW tissues. Genes related to apoptosis like FOXM1, CDK1, CDK4, Chek1, and MCM10 showed consistent upregulation in CRC cell lines, cDNA arrays and TMAs when compared to normal samples. We could also detect a correlation between the differential expression of these genes and the tumor stages. CDK4, Chek1, FOXM1, and CDC25, were observed to be downregulated in the Hispanic CRC tissues. On the other hand, oxidative stress markers were not seen to be differentially expressed in the two CRC cell lines when compared to the normal cell line. However, some of the known oxidative stress markers like PRDX4, GPX1, and SOD2 were found to be upregulated in Hispanics when compared to NHW tissues. Our results suggest that some of these stress-survival pathway genes could be explored as interesting candidates for ethnicity-specific CRC biomarkers and as novel therapeutic targets in the future. Citation Format: Aditi Kulkarni, Urbashi Basnet, Abhijeet R. Patil, Rebecca DeJesus, Sourav Roy. Differential expression of stress-survival pathway genes related to Hispanic colorectal cancer disparities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3674.
Foretinib can overcome common on-target resistance mutations after capmatinib/tepotinib treatment in NSCLCs with MET exon 14 skipping mutation
Authors: Toshio Fujino, Kenichi Suda, Takamasa Koga, Akira Hamada, Shuta Ohara, Masato Chiba, Masaki Shimoji, Toshiki Takemoto, Junichi Soh, Tetsuya Mitsudomi
Journal: Journal of Hematology & Oncology (2022)

Abstract Background Capmatinib and tepotinib are guideline-recommended front-line treatments for non-small-cell lung cancer (NSCLC) patients with MET exon 14 skipping mutations ( METex14 ). However, the emergence of acquired resistance to capmatinib/tepotinib is almost inevitable partially due to D1228X or Y1230X secondary mutations of the MET. In this study, we explored agents that are active against both D1228X and Y1230X MET to propose an ideal sequential treatment after capmatinib/tepotinib treatment failure in NSCLC patients with METex14 . Methods The inhibitory effects of 300 drugs, including 33 MET-TKIs, were screened in Ba/F3 cells carrying METex14 plus MET D1228A/Y secondary mutations. The screen revealed four-candidate type II MET-TKIs (altiratinib, CEP-40783, foretinib and sitravatinib). Therefore, we performed further growth inhibitory assays using these four MET-TKIs plus cabozantinib and merestinib in Ba/F3 cells carrying MET D1228A/E/G/H/N/V/Y or Y1230C/D/H/N/S secondary mutations. We also performed analyses using Hs746t cell models carrying METex14 (with mutant allele amplification) with/without D1228X or Y1230X in vitro and in vivo to confirm the findings. Furthermore, molecular dynamics (MD) simulations were carried out to examine differences in binding between type II MET-TKIs. Results All 6 type II MET-TKIs were active against Y1230X secondary mutations. However, among these 6 agents, only foretinib showed potent activity against D1228X secondary mutations of the MET in the Ba/F3 cell and Hs746t in vitro model and Hs746t in vivo model, and CEP-40783 and altiratinib demonstrated some activity. MD analysis suggested that the long tail of foretinib plays an important role in binding D1228X MET through interaction with a residue at the solvent front (G1163). Tertiary G1163X mutations, together with L1195F/I and F1200I/L, occurred as acquired resistance mechanisms to the second-line treatment foretinib in Ba/F3 cell models. Conclusions The type II MET-TKI foretinib may be an appropriate second-line treatment for NSCLCs carrying METex14 after campatinib/tepotinib treatment failure by secondary mutations at residue D1228 or Y1230.
Abstract 517: Protein disulfide isomerase as a predictive biomarker for non-muscle invasive bladder cancer recurrence
Authors: Kit L. Yuen, Chia-Hao Wu, Christopher R. Silvers, Alexis R. Steinmetz, Hiroshi Miyamoto, Edward M. Messing, Yi-Fen Lee
Journal: Cancer Research (2022)

Abstract INTRODUCTION AND OBJECTIVE: High recurrence rates found in non-muscle invasive bladder cancer (NMIBC) pose a financial and psychological burden for patients. We demonstrated that bladder cancer (BC) cells release protein disulfide isomerase (PDI), a redox-regulated ER-resident protein, via extracellular vesicles (EVs) when experiencing high levels of ER stress for their own survival. Chronic exposure to PDI-enriched BC EVs induced malignant transformation in recipient non-transformed cells. We hypothesized that the dynamic redox state in BC cells determines PDI cellular localization and tumors with elevated PDI preferentially incorporate PDI into EVs for removal. Furthermore, PDI expression levels and subcellular localization in tumors from NMIBC patients may predict NMIBC recurrence. METHODS: Retrospective chart review identified 122 patients with newly diagnosed low-grade NMIBC classified into 2 groups: recurrent (N=55) and non-recurrent (N=67) during follow-up period. Formalin fixed paraffin embedded tumor specimens from index transurethral resection of bladder tumor (TURBT) were obtained and a tissue microarray (TMA) was constructed. Immunofluorescent staining of TMA sections was conducted using antibodies against PDI and BiP, an ER stress marker. Stained tissues were photographed and tumor regions in each field were manually masked and confirmed by a genitourinary pathologist. Within each tumor region, total antibody labeling was determined by measuring the mean pixel intensity values with NIH ImageJ/Fiji. Manders coefficient was used to assess the colocalization of epitopes using JACoP plugin in ImageJ. RESULTS: Tumor tissues from patients that recurred expressed significantly higher levels of PDI and BiP. Moreover, high PDI and BiP expression predicted worse recurrence-free survival. These data suggest that tissues under higher levels of ER stress—as indicated by higher levels of PDI and BiP expression—have a higher risk of recurrence. Significantly higher levels of PDI were detected in non-ER cytosol in recurrent cohort tumors. CONCLUSIONS: This study provides a novel mechanism for BC recurrence and valuable clinical predictive biomarkers for NMIBC recurrence and progression. Future clinical applications targeting this pathway may be an avenue to prevent NMIBC recurrence. Citation Format: Kit L. Yuen, Chia-Hao Wu, Christopher R. Silvers, Alexis R. Steinmetz, Hiroshi Miyamoto, Edward M. Messing, Yi-Fen Lee. Protein disulfide isomerase as a predictive biomarker for non-muscle invasive bladder cancer recurrence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 517.
Abstract 1402: Monitoring the concentration of cGAMP using homogenous bioluminescent HTS-formatted assay
Authors: Said A. Goueli, kevin Hsiao
Journal: Cancer Research (2022)

Abstract Genomic instability engages the cGAS (cytosolic DNA sensor cyclic AMP-GMP synthase)-STING (stimulator of interferon genes) signaling (cGAS-cGAMP-STI NG) pathway on both sides of cancer either by being instrumental for antitumor immunity and blocking malignancy or by promoting inflammation-driven carcinogenesis and metastasis. The cGAS-STING axis also plays an essential role in initiating host immune defense against microbial invasion and STING-deficient mice are more susceptible to some viral infections. Credible evidence suggests that the cGAS-cGAMP-STI NG pathway makes fundamental contributions to at least three major cancer therapies, radiation therapy, chemotherapy, immunotherapy, and thus represents a promising pharmaceutical target. cGAS is well-positioned to act as a DNA sensor that triggers innate immune responses through production of the second messenger cyclic GMP-AMP (cGAMP) upon binding to DNA and initiating host immune responses against pathogens and cancer. However, inappropriate activation of STING signaling causes severe and often fatal autoimmune or autoinflammatory diseases. Hence, STING is an attractive drug target for the treatment of STING-driven autoimmune and inflammatory disorders. Therefore, there is a need to identify lead compounds that effectively inhibit human STING for further drug development. An attempt to search for such molecules have been described recently with the report on a STING-specific inhibitor that showed high efficiency, specificity, and safety, paving the way for therapeutically manipulating STING-mediated clinical diseases. Towards this goal, we have developed a bioluminescent assay to monitor the concentration of cGAMP in intracellular as well as extracellular compartments. The assay relies on the use of ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) to release AMP which can be converted to ATP via a coupled enzyme reaction. The ATP generated can be quantified using luciferase/luciferin detection reagents. The assay is homogenous, HTS formatted and can be completed in less than one hour. The assay is sensitive and can detect as low as 10 nM cGAMP. We will show data on the use of agents that stimulate GAS activity such as dsDNA, and the use of reporter assays to detect cytokine release upon cGAS-STING activation. Citation Format: Said A. Goueli, kevin Hsiao. Monitoring the concentration of cGAMP using homogenous bioluminescent HTS-formatted assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1402.
Computational drug repurposing based on electronic health records: a scoping review
Authors: Nansu Zong, Andrew Wen, Sungrim Moon, Sunyang Fu, Liwei Wang, Yiqing Zhao, Yue Yu, Ming Huang, Yanshan Wang, Gang Zheng, Michelle M. Mielke, James R. Cerhan, Hongfang Liu
Journal: npj Digital Medicine (2022)

Abstract Computational drug repurposing methods adapt Artificial intelligence (AI) algorithms for the discovery of new applications of approved or investigational drugs. Among the heterogeneous datasets, electronic health records (EHRs) datasets provide rich longitudinal and pathophysiological data that facilitate the generation and validation of drug repurposing. Here, we present an appraisal of recently published research on computational drug repurposing utilizing the EHR. Thirty-three research articles, retrieved from Embase, Medline, Scopus, and Web of Science between January 2000 and January 2022, were included in the final review. Four themes, (1) publication venue, (2) data types and sources, (3) method for data processing and prediction, and (4) targeted disease, validation, and released tools were presented. The review summarized the contribution of EHR used in drug repurposing as well as revealed that the utilization is hindered by the validation, accessibility, and understanding of EHRs. These findings can support researchers in the utilization of medical data resources and the development of computational methods for drug repurposing.
Abstract 4144: An AI-based, automated workflow for identification and scoring of invasive tumors in Ki-67 stained breast cancer specimens
Authors: Bhavika Patel, Stephanie Allen, Sameer Talwalkar, Navi Mehra, Jeppe Thagaard, Thomas W. Ramsing, Agnete Overgaard, Jenifer Caldara
Journal: Cancer Research (2022)

Abstract Understanding the rate of tumor cell growth in breast cancer specimens may be indicative of disease aggressiveness, a tumor characteristic which can be used to make an informed treatment decision. The nuclear protein Ki-67 is increased in cells as they prepare to divide or proliferate and is therefore widely used as a proliferation marker for tumor progression. This degree of tumor cell proliferation, or the proliferative index, is commonly detailed in pathology reports shared with the patient care team. In this study, we utilized the Ki-67 [K2] immunohistochemistry (IHC) assay to stain 10 breast cancer specimens. Stained slides were imaged using the AT2 scanner (Leica Biosystems, Buffalo Grove, IL) and analyzed using the Visiopharm Image Analysis platform. Previous efforts to assess Ki-67 positivity utilizing image analysis have relied on the use of a secondary stain or manual effort by the pathologist to exclude non-invasive tumor regions. These antiquated methods are costly to the lab as they require additional materials or valuable pathologist time. Our novel image analysis approach utilizes artificial intelligence (AI) to automatically denote non-invasive verses invasive tumor regions, which can then be used to quantify the Ki-67 proliferative index. This valuable tool will allow for greater accuracy, cost-savings, and time efficiency when analyzing breast cancer samples compared to traditional methods. Citation Format: Bhavika Patel, Stephanie Allen, Sameer Talwalkar, Navi Mehra, Jeppe Thagaard, Thomas W. Ramsing, Agnete Overgaard, Jenifer Caldara. An AI-based, automated workflow for identification and scoring of invasive tumors in Ki-67 stained breast cancer specimens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4144.
Abstract 933: Macrophage-derived C/EBPb promotes breast tumorigenesis
Authors: Alexa M. Dow, Michelle D. Rojo, Scout M. Treadwell, Heather L. Machado
Journal: Cancer Research (2022)

Abstract Breast cancer growth and progression relies on complex interactions between tumor cells and surrounding stromal cells, including immune cells. Infiltrating immune cells, including macrophages, have been shown to promote tumor progression and metastasis, and efforts have aimed at the tumor microenvironment as a therapeutic strategy. Although tumor-promoting roles of macrophages are well-established, the specific macrophage factors and transcription factor-mediated regulatory programs that drive breast cancer progression are less understood. Using a p53-/- syngeneic model of premalignant progression to invasive cancer, we identified distinct subpopulations of macrophages that resemble both normal tissue resident macrophages and tumor-associated macrophages. Interestingly, most of these macrophage subsets highly express C/EBPβ, suggesting a global function of C/EBPβ in macrophages. C/EBPβ is a transcription factor that is overexpressed in breast cancer tissues and is important for monocyte differentiation and myeloid-derived suppressor cell function. To address the function of macrophage C/EBPβ during tumorigenesis, Cebpb-floxed mice were bred to iCsf1r-Cre mice to generate mice (CebpbΔM) where Cebpb is selectively deleted in macrophages (CSF1R-expressing myeloid cells). Genetic ablation of macrophage C/EBPβ in premalignant lesions results in a significant decrease in progression to invasive cancer. In established claudin-low tumors, deletion of macrophage C/EBPβ results in decreased tumor latency and the re-expression of cytokeratin 8+E-cadherin+ cells, reminiscent of luminal-like tumors. This phenoytpe was recapitulated in an ex vivo 3D co-culture model, where uniformly round structures that lack mesenchymal projections form in the presence of CebpbΔM BMDMs. These data suggest that macrophage C/EBPβ may help maintain a mesenchymal phenotype in claudin-low tumors. Ongoing studies are aimed at identifying the Cebpb-induced gene networks in macrophages that mediate tumor progression. These studies will have critical implications for whether inhibition of C/EBPβ-regulated genes may revert claudin-low tumors to a luminal-like phenotype, rendering tumors responsive to current therapies. This work is supported by NIH R01CA212518 (H.L.M.). Citation Format: Alexa M. Dow, Michelle D. Rojo, Scout M. Treadwell, Heather L. Machado. Macrophage-derived C/EBPb promotes breast tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 933.
A systematic review and narrative synthesis of mental imagery tasks in people with an intellectual disability: Implications for psychological therapies
Authors: Olivia Mary Hewitt, Craig Steel, Susie A. Hales, Nikita Hayden, Hatice Gundeslioglu, Katherine Tapp, Peter Langdon
Journal: Clinical Psychology Review (2022)

Mental imagery is recognised for its role in both psychological distress and wellbeing, with mental imagery techniques increasingly being incorporated into psychological interventions. In this systematic review and narrative synthesis (PROSPERO 2021: CRD42021240930), we identify and evaluate the evidence base for the phenomenon and phenomenology of mental imagery in people with intellectual disabilities, to ascertain the applicability of such interventions for this population. Electronic searches of nine databases and grey literature identified relevant publications. Two reviewers independently assessed titles and abstracts of retrieved records (n = 8609) and full-text articles (n = 101) against eligibility criteria. Data were extracted and quality appraised. Forty-onepapers met our eligibility criteria. The quality and designs were variable. Mental imagery was facilitated through ensuring participants understood tasks, providing opportunity to rehearse tasks (including using concrete prompts) and using scaffolding to help participants elaborate their responses. People with intellectual disabilities can engage with mental imagery, with appropriate adaptations, although the associated phenomenology has not been thoroughly investigated. Mental imagery interventions may be useful for people with intellectual disabilities with appropriate modifications.